If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ), 'gf_id' => 'HOM05D001346', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001346' ), 'data_identifier' => 'HOM05D001346', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001346', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p38280' => 'bna', 'A02p40090' => 'bna', 'A03p21700' => 'bna', 'A03p60940' => 'bna', 'A04p05200' => 'bna', 'A06p31300' => 'bna', 'A06p35570' => 'bna', 'A06p38080' => 'bna', 'A07p22180' => 'bna', 'A07p22190' => 'bna', 'A09p02070' => 'bna', 'A09p47570' => 'bna', 'A10p05810' => 'bna', 'Aa31LG11G4030' => 'aar', 'Aa31LG11G8570' => 'aar', 'Aa31LG5G20790' => 'aar', 'Aa31LG5G2270' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1203' => 'aag', 'Actinidia03568' => 'ach', 'Actinidia14153' => 'ach', 'Actinidia18362' => 'ach', 'Actinidia32804' => 'ach', 'Ah.04g162320' => 'amhyb', 'Ah.06g192350' => 'amhyb', 'Ah.11g044020' => 'amhyb', 'AL5G35700' => 'aly', 'AL6G36440' => 'aly', 'AL6G40790' => 'aly', 'AL6G50410' => 'aly', 'Aqoxy5G00366' => 'aox', 'Aqoxy7G02713' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1EXE5V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.22TBTR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4SA7RY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9PR62B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EQL16Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W16IV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WGS0P4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0EWEF' => 'arhy', 'AT3G54620' => 'ath', 'AT4G02640' => 'ath', 'AT5G24800' => 'ath', 'AT5G28770' => 'ath', 'ATR0626G127' => 'atr', 'ATR0665G150' => 'atr', 'Atru.chr10.874' => 'acertr', 'Atru.chr2.814' => 'acertr', 'Atru.chr5.1555' => 'acertr', 'Atru.chr7.2679' => 'acertr', 'AUR62001010' => 'cqu', 'AUR62004948' => 'cqu', 'AUR62020638' => 'cqu', 'AUR62038742' => 'cqu', 'BcaB01g00174' => 'bca', 'BcaB01g02024' => 'bca', 'BcaB01g03623' => 'bca', 'BcaB02g07729' => 'bca', 'BcaB02g08449' => 'bca', 'BcaB07g29923' => 'bca', 'BcaB07g34173' => 'bca', 'BcaC01g05508' => 'bca', 'BcaC01g05510' => 'bca', 'BcaC01g05514' => 'bca', 'BcaC02g09056' => 'bca', 'BcaC03g15456' => 'bca', 'BcaC03g17749' => 'bca', 'BcaC03g17944' => 'bca', 'BcaC04g24004' => 'bca', 'BcaC06g30687' => 'bca', 'BcaC07g39805' => 'bca', 'BcaC08g44690' => 'bca', 'BcaNung01255' => 'bca', 'BcaNung02111' => 'bca', 'BolC2t09171H' => 'bol', 'BolC2t11834H' => 'bol', 'BolC2t12060H' => 'bol', 'BolC3t14957H' => 'bol', 'BolC4t25369H' => 'bol', 'BolC6t37411H' => 'bol', 'BolC7t44550H' => 'bol', 'BolC7t44826H' => 'bol', 'BolC8t50587H' => 'bol', 'BraA02t08809Z' => 'bra', 'BraA02t08972Z' => 'bra', 'BraA03t11405Z' => 'bra', 'BraA06t26482Z' => 'bra', 'BraA06t26723Z' => 'bra', 'BraA09t35856Z' => 'bra', 'BraA09t40213Z' => 'bra', 'BraA10t42842Z' => 'bra', 'C02p31280' => 'bna', 'C02p57610' => 'bna', 'C02p60050' => 'bna', 'C03p25700' => 'bna', 'C06p22260' => 'bna', 'C07p40130' => 'bna', 'C07p42970' => 'bna', 'C08p29760' => 'bna', 'C09p02160' => 'bna', 'CAN.G134.98' => 'can', 'CAN.G56.19' => 'can', 'CAN.G940.2' => 'can', 'CANSAT01G1799' => 'cansat', 'CANSAT25G2088' => 'cansat', 'CARHR164520' => 'chi', 'CARHR185330' => 'chi', 'CARHR188660' => 'chi', 'CARHR250930' => 'chi', 'CARHR250940' => 'chi', 'Carub.0005s2122' => 'cru', 'Carub.0006s2265' => 'cru', 'Carub.0006s2602' => 'cru', 'Carub.0006s3449' => 'cru', 'Ca_09422_v3' => 'car', 'Ca_10046_v3' => 'car', 'Ca_12827_v3' => 'car', 'Ca_15633_v3' => 'car', 'Ca_29791_v3' => 'car', 'CBR_g29348' => 'cbr', 'CBR_g39153' => 'cbr', 'CBR_g46185' => 'cbr', 'CBR_g55475' => 'cbr', 'Cc00_g11390' => 'ccan', 'Cc02_g30660' => 'ccan', 'CDE02G2892' => 'cde', 'CDE03G0031' => 'cde', 'CDE04G1911' => 'cde', 'CDE06G1603' => 'cde', 'CDE06G1847' => 'cde', 'CDE07G1231' => 'cde', 'Cfa002319' => 'cfa', 'Cfa006423' => 'cfa', 'Cfa011722' => 'cfa', 'Cfa013319' => 'cfa', 'Ciclev10001051m.g' => 'ccl', 'Ciclev10008515m.g' => 'ccl', 'Ciclev10020133m.g' => 'ccl', 'CiPaw.04G181300' => 'cil', 'CiPaw.07G067200' => 'cil', 'CiPaw.07G209100' => 'cil', 'CiPaw.08G021900' => 'cil', 'CiPaw.08G123700' => 'cil', 'ClCG02G016610' => 'cla', 'ClCG03G016420' => 'cla', 'ClCG08G012480' => 'cla', 'ClCG09G007460' => 'cla', 'COL.COLO4_00301' => 'col', 'COL.COLO4_06086' => 'col', 'COL.COLO4_06088' => 'col', 'COL.COLO4_15347' => 'col', 'Cpa.g.sc117.90' => 'cpa', 'Cpa.g.sc244.3' => 'cpa', 'Cpa.g.sc52.101' => 'cpa', 'CsaV3_1G039550' => 'csa', 'CsaV3_2G004160' => 'csa', 'CsaV3_2G031180' => 'csa', 'CsaV3_7G027650' => 'csa', 'CSS0019127' => 'camsi', 'CSS0028076' => 'camsi', 'CSS0032436' => 'camsi', 'CSS0049111' => 'camsi', 'DCAR_000690' => 'dca', 'DCAR_004549' => 'dca', 'DCAR_006652' => 'dca', 'DCAR_011307' => 'dca', 'DCAR_018650' => 'dca', 'DCAR_022257' => 'dca', 'Dinv00584' => 'din', 'Dinv04732' => 'din', 'Dinv10013' => 'din', 'Dinv12963' => 'din', 'Dinv14506' => 'din', 'Dinv14508' => 'din', 'Duzib128G1751' => 'dzi', 'Duzib138G1464' => 'dzi', 'Duzib150G0636' => 'dzi', 'Duzib168G1031' => 'dzi', 'Duzib177G0281' => 'dzi', 'Duzib211G0263' => 'dzi', 'ECA232G3692' => 'eca', 'ECA240G2878' => 'eca', 'EL10Ac2g03702' => 'bvu', 'EL10Ac4g09138' => 'bvu', 'EL10Ac6g14710' => 'bvu', 'EL10As6g23667' => 'bvu', 'Eucgr.B01486' => 'egr', 'Eucgr.C03986' => 'egr', 'Eucgr.H04338' => 'egr', 'FAN02G0124' => 'fan', 'FAN05G3321' => 'fan', 'FAN09G4362' => 'fan', 'FAN14G2404' => 'fan', 'FAN15G0052' => 'fan', 'FAN15G3714' => 'fan', 'FAN20G2174' => 'fan', 'FAN24G3107' => 'fan', 'FAN27G0859' => 'fan', 'FAN27G3194' => 'fan', 'FvH4_2g22580' => 'fve', 'FvH4_2g36400' => 'fve', 'FvH4_6g02940' => 'fve', 'Glyma.03G247100' => 'gma', 'Glyma.04G078300' => 'gma', 'Glyma.06G079800' => 'gma', 'Glyma.10G162100' => 'gma', 'Glyma.14G139700' => 'gma', 'Glyma.17G188500' => 'gma', 'Glyma.19G244800' => 'gma', 'Glyma.20G224500' => 'gma', 'Gohir.A06G107300' => 'ghi', 'Gohir.A08G062300' => 'ghi', 'Gohir.A08G187900' => 'ghi', 'Gohir.A08G215500' => 'ghi', 'Gohir.A11G126800' => 'ghi', 'Gohir.A11G248500' => 'ghi', 'Gohir.D06G109500' => 'ghi', 'Gohir.D07G001033' => 'ghi', 'Gohir.D08G071400' => 'ghi', 'Gohir.D08G206200' => 'ghi', 'Gohir.D08G232200' => 'ghi', 'Gohir.D11G132300' => 'ghi', 'Gohir.D11G259400' => 'ghi', 'Gorai.001G000600' => 'gra', 'Gorai.004G075400' => 'gra', 'Gorai.004G218300' => 'gra', 'Gorai.004G246700' => 'gra', 'Gorai.007G141500' => 'gra', 'Gorai.007G277300' => 'gra', 'Gorai.010G124200' => 'gra', 'GSVIVG01000714001' => 'vvi', 'GSVIVG01021790001' => 'vvi', 'GSVIVG01035557001' => 'vvi', 'HanXRQChr03g0082851' => 'han', 'HanXRQChr09g0258861' => 'han', 'HanXRQChr12g0381601' => 'han', 'HanXRQChr13g0397661' => 'han', 'HanXRQChr13g0412021' => 'han', 'HanXRQChr15g0486601' => 'han', 'Haze_04362' => 'cav', 'Haze_21805' => 'cav', 'Haze_24524' => 'cav', 'Hma1.2p1_0817F.1_g223100' => 'hma', 'HPP92_010179' => 'vpl', 'HPP92_010180' => 'vpl', 'HPP92_010247' => 'vpl', 'HPP92_010248' => 'vpl', 'HPP92_010275' => 'vpl', 'HPP92_021889' => 'vpl', 'HPP92_026289' => 'vpl', 'Hund03268' => 'sun', 'Hund06969' => 'sun', 'Hund19307' => 'sun', 'Hund22114' => 'sun', 'Lalb_Chr02g0148821' => 'lal', 'Lalb_Chr06g0168061' => 'lal', 'Lalb_Chr06g0168071' => 'lal', 'Lalb_Chr08g0243411' => 'lal', 'Lalb_Chr23g0269321' => 'lal', 'Lj1g0023247' => 'lja', 'Lj1g0027014' => 'lja', 'Lj5g0014207' => 'lja', 'Lj7A753T39' => 'lonja', 'Lj9A662G26' => 'lonja', 'Lsat_1_v5_gn_1_73280' => 'lsa', 'Lsat_1_v5_gn_5_58820' => 'lsa', 'Lsat_1_v5_gn_8_115900' => 'lsa', 'Manes.01G202200' => 'mes', 'Manes.03G001600' => 'mes', 'Manes.05G083900' => 'mes', 'Manes.08G134500' => 'mes', 'Manes.09G153300' => 'mes', 'Manes.16G137300' => 'mes', 'Mapoly0012s0172' => 'mpo', 'MBI04_g08414_MAGBIO' => 'mbi', 'MBI11_g15910_MAGBIO' => 'mbi', 'MBI13_g31552_MAGBIO' => 'mbi', 'MCO08G213' => 'mco', 'MD04G1224400' => 'mdo', 'MD05G1206400' => 'mdo', 'MD08G1123300' => 'mdo', 'MD10G1193400' => 'mdo', 'MD12G1241100' => 'mdo', 'MD15G1102300' => 'mdo', 'Medtr1g008990' => 'mtr', 'Medtr1g080920' => 'mtr', 'Medtr3g109310' => 'mtr', 'Medtr3g110010' => 'mtr', 'Medtr7g115120' => 'mtr', 'Medtr7g115140' => 'mtr', 'MELO3C004378.2' => 'cme', 'MELO3C011167.2' => 'cme', 'MELO3C015377.2' => 'cme', 'MELO3C015754.2' => 'cme', 'Migut.B01086' => 'egut', 'Migut.E01416' => 'egut', 'Migut.N01912' => 'egut', 'MSTRG.13936' => 'ama', 'MSTRG.1615' => 'ama', 'MSTRG.20444' => 'ama', 'MSTRG.28020' => 'ama', 'Nitab4.5_0000087g0220' => 'nta', 'Nitab4.5_0000087g0230' => 'nta', 'Nitab4.5_0001592g0050' => 'nta', 'Nitab4.5_0003259g0120' => 'nta', 'Nitab4.5_0003279g0020' => 'nta', 'Nitab4.5_0003279g0030' => 'nta', 'Nitab4.5_0014012g0010' => 'nta', 'Nitab4.5_0028413g0010' => 'nta', 'Nn1g02540' => 'nnu', 'Nn2g12732' => 'nnu', 'Nn3g19494' => 'nnu', 'Nn6g32035' => 'nnu', 'Nn8g41004' => 'nnu', 'Oeu002658.2' => 'oeu', 'Oeu016439.1' => 'oeu', 'Oeu027468.1' => 'oeu', 'Oeu038305.1' => 'oeu', 'Oeu038442.2' => 'oeu', 'Oeu048005.1' => 'oeu', 'Os02g0175100' => 'osa', 'Os02g0266800' => 'osa', 'Os03g0796900' => 'osa', 'Os06g0662200' => 'osa', 'Os07g0182000' => 'osa', 'Os12g0601800' => 'osa', 'Peaxi162Scf00045g01458' => 'pax', 'Peaxi162Scf00071g00088' => 'pax', 'Peaxi162Scf00282g00338' => 'pax', 'Peaxi162Scf00385g00611' => 'pax', 'Peaxi162Scf00621g00411' => 'pax', 'Peaxi162Scf02674g00003' => 'pax', 'PGR004G2685' => 'pgr', 'PGR044G1653' => 'pgr', 'PGSC0003DMG400014858' => 'stu', 'PGSC0003DMG400019455' => 'stu', 'Phvul.001G077200' => 'pvu', 'Phvul.006G101700' => 'pvu', 'Phvul.007G187400' => 'pvu', 'Phvul.009G104100' => 'pvu', 'Phvul.011G101200' => 'pvu', 'Potri.002G045800' => 'ptr', 'Potri.005G053200' => 'ptr', 'Potri.005G217500' => 'ptr', 'Potri.006G277800' => 'ptr', 'Potri.013G040700' => 'ptr', 'Pp3c15_18260' => 'ppa', 'Pp3c15_18270' => 'ppa', 'Pp3c15_7040' => 'ppa', 'Pp3c9_2770' => 'ppa', 'Pp3c9_2771' => 'ppa', 'Pp3c9_6339' => 'ppa', 'Pp3c9_6350' => 'ppa', 'PRCOL_00005631' => 'pco', 'Prupe.1G455300' => 'ppe', 'Prupe.6G343100' => 'ppe', 'Prupe.8G232800' => 'ppe', 'Psat3g007160' => 'psa', 'Psat5g023160' => 'psa', 'Psat6g006040' => 'psa', 'Psat6g144640' => 'psa', 'PSO063G0752' => 'pso', 'PSO170G2213' => 'pso', 'PSO210G0790' => 'pso', 'PSO210G6449' => 'pso', 'PSO461G0023' => 'pso', 'PSO832G4214' => 'pso', 'QL03p025824' => 'qlo', 'QL03p026231' => 'qlo', 'QL04p007431' => 'qlo', 'QL12p025990' => 'qlo', 'QL12p042295' => 'qlo', 'QL12p042624' => 'qlo', 'RcHm_v2.0_Chr3g0451141' => 'rch', 'RcHm_v2.0_Chr6g0289641' => 'rch', 'RcHm_v2.0_Chr6g0305501' => 'rch', 'Rhsim07G0075400' => 'rsi', 'Rhsim07G0170900' => 'rsi', 'Sabra01G0127700' => 'sbr', 'Sabra02G0036700' => 'sbr', 'Sabra05G0046700' => 'sbr', 'Sabra05G0166700' => 'sbr', 'Sabra06G0215400' => 'sbr', 'Sabra13G0037600' => 'sbr', 'SalBow4G2598' => 'sbo', 'SalBow4G3295' => 'sbo', 'Sc09g0003910' => 'sci', 'Sc09g0007330' => 'sci', 'Sc20g0000310' => 'sci', 'Sed0003325' => 'sed', 'Sed0003818' => 'sed', 'Sed0011676' => 'sed', 'Sed0011981' => 'sed', 'Sed0015023' => 'sed', 'Sed0026731' => 'sed', 'Sed0027418' => 'sed', 'SEGI_03575' => 'sgi', 'SGA_v2.0_scaffold27G11656' => 'sas', 'SGA_v2.0_scaffold54G19475' => 'sas', 'SGA_v2.0_scaffold80G25906' => 'sas', 'SGA_v2.0_scaffold81G26089' => 'sas', 'SMO364G0162' => 'smo', 'Solyc01g097330.3' => 'sly', 'Solyc08g006110.4' => 'sly', 'Solyc08g022080.4' => 'sly', 'Solyc08g022110.2' => 'sly', 'Sopen01g041000' => 'spe', 'Sopen08g002080' => 'spe', 'Sopen08g007600' => 'spe', 'Sp2g20050' => 'spa', 'Sp2g22650' => 'spa', 'Sp4g21260' => 'spa', 'Sp5g07830' => 'spa', 'Sp6g02550' => 'spa', 'TAR362G0578' => 'tar', 'TAR383G0844' => 'tar', 'TAR626G1392' => 'tar', 'TAR633G1863' => 'tar', 'THA.LOC104799003' => 'tha', 'THA.LOC104799677' => 'tha', 'THA.LOC104799951' => 'tha', 'THA.LOC104802830' => 'tha', 'THA.LOC104804691' => 'tha', 'THA.LOC104810652' => 'tha', 'THA.LOC104814964' => 'tha', 'THA.LOC104815936' => 'tha', 'THA.LOC104820087' => 'tha', 'THA.LOC104821675' => 'tha', 'Thecc.01G268400' => 'tca', 'Thecc.05G283600' => 'tca', 'Thecc.09G003800' => 'tca', 'Thhalv10004611m.g' => 'esa', 'Thhalv10004701m.g' => 'esa', 'Thhalv10010426m.g' => 'esa', 'Thhalv10028688m.g' => 'esa', 'TPR.G12118' => 'tpr', 'TPR.G12949' => 'tpr', 'TPR.G1350' => 'tpr', 'TPR.G6985' => 'tpr', 'TWI12G0381' => 'twi', 'TWI12G0689' => 'twi', 'TWI18G0258' => 'twi', 'TWI32G0972' => 'twi', 'TWI56G0207' => 'twi', 'TWI63G0206' => 'twi', 'unitig_32.g10939' => 'ugi', 'unitig_32.g10940' => 'ugi', 'unitig_746.g26845' => 'ugi', 'unitig_748.g8174' => 'ugi', 'unitig_748.g8175' => 'ugi', 'unitig_899.g15582' => 'ugi', 'vmacro05098' => 'vma', 'vmacro13828' => 'vma', 'VMungo0540G0989' => 'vmu', 'VMungo0647G0611' => 'vmu', 'VMungo0647G0675' => 'vmu', 'VMungo0720G1467' => 'vmu', 'VMungo1309G2286' => 'vmu', 'Zm00001eb031210' => 'zma', 'Zm00001eb060810' => 'zma', 'Zm00001eb060860' => 'zma', 'Zm00001eb060910' => 'zma', 'Zm00001eb103600' => 'zma', 'Zm00001eb180760' => 'zma', 'Zm00001eb212940' => 'zma', 'Zm00001eb233420' => 'zma', 'Zm00001eb301570' => 'zma', 'Zm00001eb389660' => 'zma' ) $gf_id = 'HOM05D001346' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001346' ) $data_identifier = 'HOM05D001346' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 22, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 4, 'ccan' => (int) 2, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 13, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 5, 'oeu' => (int) 6, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 2, 'stu' => (int) 2, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 10, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 6, 'vma' => (int) 2, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb389660' $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